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III. Discriminational Ability of Fingerprinting Techniques

III. Discriminational Ability of Fingerprinting Techniques

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FINGERPRINTING CROP VARIETIES



109



even with classical breeding techniques, a few back-cross generations, on

average, shift the genotype rapidly closer to the recurrent parent.



2. The Effect of the Breadth of the Germplasm Base Used in Seed

Production and Agriculture

The degree to which identical or very genetically similar parents are used

in commercial seed production for F1 hybrid crops or varieties also determines the degree of genetic difference between cultivars. For example, in

the United States and Europe, numerous breeding organizations have

produced commercial F1seed using at least one common publicly available

inbred line per hybrid. In the United States, the public lines B73, B37,

B14, A632, Oh43, and Mo17 have been widely used. In France the line F2

is very extant in agriculture. In the United States, each foundation seed

company supplies customers from common sources of inbred lines. These

lines can be used as parents in many single-cross maize hybrids. There is

the possibility that numerous maize hybrids sold by different organizations

could be identical genetically and, therefore, be impossible to differentiate

by even the most discriminative fingerprinting techniques.



3. The Effect of Descriptor Class and Separation Method on the

Ability to Reveal Genetic Diversity

Not all protein fractions have an equal prevalence of diverse proteins.

Each cultivated species must be individually investigated to find the class or

classes of protein that reveal the most genetic variation. Isozymes generally

show variability for several enzyme systems, and when a number of systems are used, the level of discrimination between cultivars can be appreciable. Alcohol-soluble seed storage proteins generally also reveal significant diversity. Water- and salt-soluble proteins can also reveal variability

among cultivars, but generally these profiles are qualitatively and quantitatively very complex, probably affected by the stage of physiological development, and usually are not well understood genetically. For these

reasons, one-dimensional separations of such complex protein mixtures,

therefore, are not usually relied upon as descriptors. However, with the

advent of improved two-dimensional separation methods, coupled with an

enhanced ability to identify and quantify individual spots and complex spot

patterns through sophisticated software packages, it is possible to database

multiple images. Comparisons can then be made using profiles with hundreds of spots per cultivar as descriptors (Dunbar et a!, , 1985; Gorg et al. ,



110



J. S. C. SMITH AND 0. S. SMITH



1988; Higginbotham et al., 1989a,b, 1991a,b. Generally, a specific combination of protein class and electrophoretic or chromatographic technique must be sought by screening several combinations of extraction and

separation protocols in order to find methods that will reveal the maximum

degree of variability for a set of cultivars. Oftentimes, different electrophoretic and chromatographic procedures provide complimentary identification.

At the DNA level, some cultivated species (such as maize) that are

immensely rich in genetic variation, as revealed by biochemical means, are

also highly polymorphic when surveyed for RFLPs; some species, at least

with current methodologies, for example, wheat, do not show much variation for RFLPs. More complex two-dimensional electrophoretic separations of protein may then be more appropriate to consider (Anderson

et al., 1985; Dunbar et af., 1985).



B. DISCRIMINATIONAL

ABILITYOF PROTEIN

AND DNA DESCRIPTORS

FOR SELECTED

OR CULTIVATED

SPECIES

A high degree of unique identification among cultivated varieties and

inbred lines of many species is possible by means of one or more profiling

methodologies. Development of fingerprinting technology is at various

stages for each crop, depending upon several factors. These include the

amount of genetic variation that is present within the cultivated germ

plasm, the state of technology as regards its ability to reveal variation, and

the level of need expressed by breeders, seed producers, seed certification

and registration agencies, and other interested parties to have in place

precise and unique profiles of cultivated varieties. There is a synergistic

relationship between the ability and the desire to provide fingerprints.

Even when fingerprinting ability has been achieved, for example, as in

maize, the work is incomplete. There remain improvements in the efficiency of profiling to be sought, yet further detailed profiles to be obtained for the benefit of plant breeders and geneticists, and standards of

profile derivation and usage to be evolved and accepted in the scientific,

legal, and administrational communities. The current status of profiling is,

therefore, always somewhat transient and rests upon a large body of

published research that is continuously built upon. In this review, we are

able only to present a framework of appropriate references for each major

cultivated species (Tables I and 11). For additional details, the reader is

encouraged to pursue the citations given and to keep abreast of new

information as it appears.



Table I

Summary of Laboratory-Based Cdtivar Identification Ability for Cultivated Species of Major Economic Importance

~



~



Source

material



Cultivated species



Range of genotypes



Wheat

(Trificurnsupp.)



88 most widely grown

U.S. cultivars in

1979



Gliadins



PAGE



88 varieties

licensed in Canada



Gliadins



PAGE



68 Canadian and

2 U.S. spring

wheats

51 varieties on

U.K. national list

27 spring wheats



Gliadins and

glutenins



Technique"



Profiling ability



Reference

Jones et al. (1982)



Gradient

SDS-PAGE



85% unique;

cultivars with

similar profiles

closely related by

pedigree

93% unique;

cultivars with

similar profiles

related by pedigree

84% unique

profiles



Gliadins



SGE



100% unique



Gliadins



RP-HPLC



93% unique



10 most important

U.K. cultivars

15 European

cultivars



Gliadins



100% unique



Gliadins



Rapid

RP-HPLC

RP-HPLC



Clydesdale and

Draper (1982)

Marchylo et al.

(1988)

Bietz and Cobb

(1985)

Burnouf et al.

(1983)



Many U.S. varieties



Gliadins



RP-HPLC



14 U.K. varieties



Gliadins and

glutenins



Two-dimensional

electrophoresis



All but three closely

related varieties

unique

Most unique; only

some with similar

pedigrees

indistinguishable

100% unique



Zillman and Bushuk

(1979a; b)



Marchylo et al.

(1989)



Bietz et al. (1984)



Anderson et al.

(1985)

(continues)



Table I (Continued)

Cultivated species

Maize (inbreds)

(Zea mays)



Range of genotypes

406 publicly

available inbred

lines, U.S.,

Canada, Europe

30 widely used

U.S. lines in

1975

113 Canadian lines



62 widely used U.S.

public lines,

1960-1985

14 Lancaster Sure

Crop lines



Source

material



Technique"



Protiling ability



Reference



Coleoptile

isozymes, 23

loci



SGE



73% unique



Stuber and

Goodman (1983)



Coleoptile

isozymes



SGE



93% unique



Goodman and

Stuber (1980)



Coleoptile

isozymes



SGE



80% unique



Coleoptile

isozymes, 34

loci

Coleoptile

isozymes and

zeins

Coleoptile

isozymes and

zeins

Zeins



SGE



94% unique



Cardy and

Kannenberg

(1982)

Smith ef al. (1987)



SGE and

RP-HPLC



Unique unless

related by

back-crossing

Unique unless

related by

back-crossing

92% unique



Wilson (1985)



100% unique



Wall et al. (1984)



Only split

into 2 groups

100% unique



Esen el al. (1989)



J. S. C. Smith et al.



100% unique

electrophoresis



(1991~)

Higginbottham ef al.

(1991a; b)



17 Iowa Stiff

Stalk Synthetic

lines

25 U.S. public

inbreds

9 public lines



Zeins



15 public lines



Zeins



150 public lines



DNA



37 inbred lines



Embryo

protein



SGE and

RP-HPLC

Isoelectric

focusing

Two-dimensional

electrophoresis

Immunology

RFLPs, 46

probes

Two-dimensional

electrophoresis



Smith and Smith

(1987)

Smith and Smith

(1988a)



Maize (hybrids)

(Zea mays)



SGE



94% unique



SGE



95% contrasting

profiles, some

very similar

60% unique



47 French hybrids



Coleoptile

isozymes, 22

loci

Coleoptile

isozymes, 21

loci

Coleoptile

isozymes and

zeins

Coleoptile

isozymes and

zeins

DNA



106 U.S. hybrids



DNA



RFLPs, 46

probes



174 cultivars



Coleoptile

isozymes, 11

enzymes

DNA



SGE



155 Canadian

hybrids

111 U.S. hybrids



128 U.S. hybrids



61 French hybrids



+

e

W



Soybean (Glycine

max)



58 lines



Barley (Hordeum

vulgare)



60 lines

66 cultivars



55 U.S. cultivars

88 U.K. varieties



DNA

Coleoptile

isozymes and

hordeins

Hordeins

Hordeins



SGE and

RP-HPLC

SGE and

RP-HPLC

RFLPs, 80

probes



100% different

but 14 widely used

hybrids similar

94% unique, 3

hybrids very

similar

Most unique, but

some with very

similar profiles

77% unique



Cardy and

Kannenberg

(1982)

Smith (1984)



Smith (1988)



Smith (1989)



J. S. C. Smith and

Smith (1991)

J. S. C. Smith et 01.

(1991b)



Cardy and

Beavorsdorf

(1984)

Keim et al. (1989)



RFLPs, 17

probes

RFLPs

Electro

phoresis



88% unique



Most unique

94% unique



Cregan et al. (1990)

Nielsen and

Johansen (1986)



SDS-PAGE

SDS-PAGE

and urea

acid page



44% unique

Fell into 32

groups



Heisel et al. (1986)

Shewry et al. (1978)



(continues)



Table I (Continued)

~~



~~



Cultivated species



Range of genotypes



~



~



Source

material



Technique"



Profiling ability



12 Canadian

cultivars

9 cultivars

13 cultivars



Hordeins



RP-HPLC



100% unique



Hordeins

Leaf proteins



100% unique

100% unique



40 cultivars



Hordeins



DNA probes

Two-dimensional

electrophoresis

PAGE



48 cultivars



DNA



23 RFLPs



Fell into 17

groups

Some variation



8 cultivars



Acid PAGE



100% unique



25 cultivars



Albumins and

globulins

Prolamins



29 U.S. cultivars



Prolamins



Isoelectric

focusing

RP-HPLC



27 U.S. cultivars



Glutelins



RP-HPLC



9 cultivars



DNA



70 varieties



DNA



2 human

minisatellite

probes

10 RFLPS



Fell into 4

groups

All unique if

grain type

also considered

Most unique, small

differences for

closely related

varieties

100% unique



Reference

Marchylo and

Kruger (1984)

Bunce el al. (1988)

Gorg et al. (1988)

Gebre et al. (1986)

Graner er al. (1990)



c

e



A



Rice (Oryza

sativa)



83% unique



Sarkar and Bose

(1984)

Guo et al. (1986)

Lookhart et al.

(1987)

Huebner et al.

(1990)

Dallas (1988)



Wang and Tanksley

(1989)



Oats (Avena sativa)



Sorghum (Sorghum

vulgare)



23 U.S. varieties



Prolamins



PAGE and

RP-HPLC



100% unique



U.S. varieties



DNA



RFLPS



Variation found



7 lines



Kafirins



RP-HPLC



120 breeding lines



Coleoptile

isozymes

Coleoptile

isozymes

Coleoptile

isozymes

DNA



SGE

SGE



Unrelated lines

had different

profiles

31 genotypes, 12%

lines unique

38% unique



SGE



33% unique



Schertz et al. (1990)



100 probes



100% unique



Lee et al. (1990a)



Isoelectric

focusing and

RP-HPLC

SDS-PAGE



All unique



Sastry et al. (1986)



100% unique



RFLPs, 2

probes

RFLPS, 2

probes



100% unique



Loeschcke and

Stegemann (1978)

Gebhardt et al.

(1989)

Gebhardt et al.

(1989)



37 converted lines

70 hybrids

25 elite U.S.

lines

4 lines, 2 hybrids

8 varieties

Potato (Solanurn

tuberosum)



Kafirins and

glutelins



600 cultivars



Tuber proteins



38 lines



DNA



20 varieties



DNA



100% unique



Lookhart (1985a);

Lookhart and

Pomeranz (1985b)

Hoffman et al.

(1990)

J. S . C. Smith and

Smith (1988b)

Schertz et al. (1990)

Schertz et al. (1990)



“Abbreviations: PAGE, polyacrylamide gel electrophoresis; SGE, starch gel electrophoresis; RP-HPLC, reverse-phase high-performance

liquid chromatography; RFLPs, restriction fragment length polymorphisms; SDS, sodium dodecyl sulfate.



Table II

Additional Examples of Laboratory-Based Cultivar Identification



Genus



Species



Common name



AIlium



SPP.



Onion



Arachb

Beta

Brassica



SPP.

vulgatis

SPP.



Peanut

Beet

Brassicas



napus

oleracea



Rape

Cabbage, etc.



Pepper

Pecan

Coffee

Orange, grapefruit, etc.



Capsicum

Carya



Coflea

Citrus



Cucurbira

Festuca



sativus

SPP.



Cucumber

Fescue



Source material

Protein

Protein

DNA

DNA

Protein

Protein

DNA

Protein

Protein

Protein

Protein

Protein

DNA

Protein

Protein

DNA

DNA

Protein and DNA

DNA

Protein

Protein



Reference

Nakamura and Tahara (1977)

Hadacova et al. (1981)

Havey (1990)

Halward er al. (1990)

Nagamine et al. (1989)

Coulthart and Denford (1982)

Nakamura (1977)

Slocum er al. (1990)

Gupta and Robbelen (1986)

Arus er al. (1982)

Woods and Thurman (1976)

Wills el al. (1979)

Wills and Wiseman (1980)

Livneh ef al. (1990)

Eugene and Wolfe (1982)

Bade and Stegemann (1982)

Durham et al. (1990)

Jarrell and Roose (1990)

Liou et al. (1990)

Kennard et al. (1990)

Hicks et al. (1982)

Villamil et al. (1982)

Abernethy et al. (1989)



Fragaria



manassa



Gossypium



Strawbeny



Protein



Cotton



Protein

Protein

DNA

DNA

Protein

DNA

DNA

Protein

Protein

Protein

Protein

Protein

Protein

Protein

DNA

DNA

Protein

Protein

DNA

Protein

Protein



Helianthus

Humulus

Juglans

Lactuca



lupulus

SPP.

sativa



Sunflower

HOP

Walnut

Lettuce



Lens

Lolium



culinaris

SPP.



Lentil

Ryegrass



Malus



SPP.



Apple



Medicago



SPP.



Alfalfa, lucerne



Olea



europaea



Olive



annuus



Bnnghurst et al. (1981)

Drawert et al. (1974)

Kapse and Nerkar (1985)

Rao et al. (1990)

Khaler and Lay (1985)

Kenny et al. (1990)

Fjellstrom and Parfitt (1990)

Kesseli and Michelmore (1986)

Landry et al. (1987)

Harvey and Muehlbauer (1989)

Hayward and McAdam (1977)

Nakamura (1979)

Arcioni et al. (1980)

Payne et al. (1980)

Ostergaard and Nielsen (1981)

Gilliland et al. (1982)

Quaite and C a d i n (1985)

Nybom and Schaal (1990)

Nybom et ul. (1990)

Bingham and Yeh (1971)

Quiros (1980, 1981)

Kidwell and Osborn (1990)

Gardiner and Forde (1988)

Pontikis et al. (1980)

(continues)



Table II (Continued)

Genus



Species



Persea

Phaseolus



americana

vulgaris



Avocado

Field bean



Pisum

Poa



sativum

pratensus



Pea

Bluegrass



Prunus



Common name



Pyrm



Peach, almond,

Cherry

Pear



Rosa

Rubus



Rose

Blackberry, raspberry



Saccharum

Secale



SPP.

cereale



Sugarcane

Rye



Vicia

Vigna

Vitis



faba



Broad (field) bean

Cowpea

Grape



SPP.

vinifera



Source material

Protein

Protein

DNA

Protein

Protein

Protein

Protein

Protein

DNA

Protein

Protein

DNA

DNA

DNA

DNA

Protein

Protein

Protein

Protein

Protein

Protein

Protein

DNA



Reference

Torres and Bergh (1980)

Hussain ef al. (1986)

Nodari et al. (1990)

Cooke (1984)

Wilkinson and Beard (1972)

Wehner ef al. (1976)

Wu et al. (1984)

Carter and Brock (1980)

Chapparo et al. (1990)

Kuhns and Fretz (1978a,b)

Santamour and Demuth (1980)

Rajapaske et al. (1990)

Nybom et al. (1989)

Moore (1990)

Nybom and Schaal (1990)

Glaszmann er al. (1989)

Steiner et al. (1984)

Ramirez and Pisabarro (1985)

Cooke (1984)

Vaillancourt and Weeden (1990)

Drawert and Gorg (1974)

Wolfe (1977)

Gogorcena et al. (1990)



FINGERPRINTING CROP VARIETIES



119



IV. USAGE OF FINGERPRINTS

A. THE

NATURE

OF PLANT

BREEDING

AND THE NEED

FOR



LONG-TERM

RESEARCH

INVESTMENT

Plant variety protection and patents are means by which intellectual

property protection can be conferred upon the end product of research

investment in plant breeding. These forms of protection are means by

which an environment suitable for the encouragement of further investment can be provided. Plant breeding is particularly dependent upon

long-term support because elite breeding programs alone can require 10

years to produce an improved variety. Investment in new technologies can

take an equal or greater time span before their practical implementation

can be effected. Investment in genetic resource conservation and utilization must be made over even greater time frames.



B. PLANTVARIETY

PROTECTION,

REGISTRATION,

CERTIFICATION,

AND PATENTS

In order for cultivars to be nationally or internationally registered and

for breeders to be granted plant breeders’ rights of protection, varieties

must successfully pass inspection for the criteria of distinctness, uniformity,

and stability (DUS) (Bailey, 1983). Certification is a test of the trueness to

declared varietal type. Application of these tests can help promote the

breeding of novel genotypes. DUS standards help ensure that the breeding

process is pursued to completion and that a seed source representing the

variety is available and can be multiplied. Other tests of agronomic performance will determine whether the new variety has a performance

advantage over existing varieties.

Traditionally, morphological data have been used to define the parameters of certification and DUS tests. However, morphological characters

whose expression is affected by environment and which exhibit continuous

distribution are notoriously poor taxonomic descriptors. Therefore, there

is growing interest in the use of biochemical and DNA-based methods to

provide more sharply defined and repeatable genotypic descriptions. A

detailed discussion of the utility of biochemical data in providing descriptors for the granting of plant breeders’ rights has been given by Bailey

(1983). In the United Kingdom, electrophoretic profiles of gliadins have

been used to compare wheat varieties for the past 10 years (Parnell, 1983).

Electrophoregrams of commonly grown wheat varieties are published



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